From 1926 to 1928, he studied economics at the University of Wisconsin in Madison in the United States, where in 1926 he married the literary historian Mildred Fish. In 1929-1930 he became a Doctor of Philosophy in Gießen, producing as his thesis Die vormarxistische Arbeiterbewegung in den Vereinigten Staaten ("The Pre-Marxist Workers' Movement in the United States"). Along with the Gießen economist Friedrich Lenz (1885–1968), he founded the Wissenschaftliche Arbeitsgemeinschaft zum Studium der sowjetischen Planwirtschaft ("Scientific Working Community for the Study of the Soviet Planned Economy"), or ARPLAN in 1931. Harnack was made First Secretary of this group, which counted about 50 members. At the height of the Great Depression, the capitalist system had clearly broken down, and the Soviet model seemed to them to be an interesting alternative. Scientists, but also ardent revolutionary nationalists like Klaus Mehnert and Ernst Jünger and communist intellectuals like George Lukacs and Karl August Wittfogel took part in sessions. Harnack's hope, apparently, was that Germany could serve as a spiritual and economic bridge between East and West. The first meeting of the group took place on 3 and 4 January 1932. In August and September of the same year a three week trip to the Soviet Union was organized with the help of the Soviet embassy in Berlin. The soviet economy was observed in Moscow, Leningrad, Odessa, Kiew and in the Dnieper region.

In 1933, after Hitler's rise to power made it necessary to dissolve ARPLAN, Harnack was given a post as a scientific expert in the Reich Economic Ministry. The same year, he also finished his legal qualifications in Jena, successfully completing the junior law examination.

Together with his wife Mildred, the writer Adam Kuckhoff and his wife Greta, Harnack assembled a discussion circle which debated political perspectives on the time after the National Socialists' expected downfall or overthrow.

In 1940-1941, the group was in contact with Soviet agents, and was trying to thwart the forthcoming German invasion of the Soviet Union. Harnack and others even sent the Soviets information about the forthcoming invasion. In 1941, Harnack published the resistance magazine Die innere Front ("The Inner Front"). At about the same time, he received information from Rudolf von Scheliha about the Final Solution.

In July 1942, the Decryption Department of the Oberkommando des Heeres managed to decode the group's radio messages, and the Gestapo pounced. On 7 September, Arvid and Mildred Harnack were arrested. Arvid Harnack was sentenced to death on 19 December after a four-day trial before the Reichskriegsgericht ("Reich Military Tribunal"), and was put to death three days later at Plötzensee Prison in Berlin. His wife was originally given six years in prison, but Hitler swiftly cancelled the sentence and ordered a new trial, which pronounced the desired death sentence. After execution, both of their bodies were released to Hermann Stieve, anatomy professor at Humboldt University, to be dissected for research. While her remains were eventually buried by a friend at the city's Zehlendorf Cemetery, the location of his is unknown.